Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDC73

Cell type

Cell type Class
Blood
Cell type
THP-6
NA
NA

Attributes by original data submitter

Sample

source_name
T-cell acute lymphoblastic leukemia
tissue
T-cell acute lymphoblastic leukemia
cell line
THP-6
chip-seq antibody
CDC73/Parafibromin (Bethyl A300-171A)
genotype
N/A
treatment
shControl
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM6858837
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked for most samples by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. For Ets1. For H3K27ac and H2K120ub1, cells were crosslinked with 1% formaldehyde at room temperature. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a QSonica Q800 bath sonicator in 0.3% SDS-containing lysis buffer. Samples were diluted 1:3.3 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples (vehicle-treated only), 1:8 diluted sonicated chromatin (whole cell extract) was added directly to the reverse crosslinking step without immunoprecipitation. Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced on the Illumina NextSeq 550 (38 bp reads) or on the Illumina NovaSeq 6000 (151 bp reads) .

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
31397830
Reads aligned (%)
95.8
Duplicates removed (%)
25.8
Number of peaks
5215 (qval < 1E-05)

hg19

Number of total reads
31397830
Reads aligned (%)
95.2
Duplicates removed (%)
26.1
Number of peaks
5080 (qval < 1E-05)

Base call quality data from DBCLS SRA